Small things in docs
KVM doc
KVM BIOS setting
Minor doc fixes
Merge branch 'master' of github.com:pjotrp/cloudbiolinux

Conflicts:
	doc/linux_kvm.md
KVM OpenSuSE URL
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
Flavor for neurodebian, a debian neuroscience package repository
It is just a flavor, not edition
Linuxbrew cannot be cloned since the base ubuntu 13.10 (from ubuntu cloud-images.ubuntu.com) does not have git installed
PyCharm broke indentation?
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
Added preliminary listing from neurodebian packages, needs cleanup
Update X tropicalis build version to xenTro3
Improve ability to handle preparation of very large genomes by avoiding command line too long issues
Check for isolated input before printing shell exports. Fixes arq5x/gemini#308
Remove poorly specified transcripts the GTF file.

This removes transcripts without gene_id and transcript_id set;
it also removes transcripts which do not have a corresponding
FASTA sequence.
Add DEXseq GFF creation.